Non-toxic could mean Low VOC. VOC's are the fumes that new paint give off.

When we built our coop we used raw linseed oil on all the 2x4 frame pieces and all the interior plywood. I painted the exterior of the coop and to be honest, I didn't use a low VOC paint. However, we didn't paint anything that the chickens have access to and we gave it a couple of days to "set."